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Coexpression cluster:C2982: Difference between revisions

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|full_id=C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum
|full_id=C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum
|id=C2982
|id=C2982
|ontology_enrichment_celltype=CL:0000066!5.07e-12!254;CL:0002076!3.49e-11!43;CL:0000223!1.84e-08!59
|ontology_enrichment_celltype=CL:0002076!1.60e-12!42;CL:0000066!1.88e-11!253;CL:0000223!4.98e-09!58;CL:0002368!3.19e-07!13
|ontology_enrichment_disease=DOID:1749!5.38e-07!14
|ontology_enrichment_disease=DOID:1749!1.56e-07!14
|ontology_enrichment_uberon=UBERON:0007023!7.94e-29!115;UBERON:0004121!4.50e-21!169;UBERON:0000924!1.38e-19!173;UBERON:0006601!1.38e-19!173;UBERON:0000153!6.30e-19!129;UBERON:0007811!6.30e-19!129;UBERON:0000033!2.16e-18!123;UBERON:0000064!8.37e-18!219;UBERON:0001049!3.91e-17!57;UBERON:0005068!3.91e-17!57;UBERON:0006241!3.91e-17!57;UBERON:0007135!3.91e-17!57;UBERON:0001017!6.48e-17!82;UBERON:0000062!2.85e-16!511;UBERON:0005743!5.71e-16!86;UBERON:0003075!8.00e-16!86;UBERON:0007284!8.00e-16!86;UBERON:0000955!1.29e-15!69;UBERON:0006238!1.29e-15!69;UBERON:0002616!5.56e-15!59;UBERON:0002346!5.34e-14!90;UBERON:0000467!9.45e-14!625;UBERON:0000480!1.59e-13!626;UBERON:0000475!3.60e-13!365;UBERON:0000481!4.80e-13!347;UBERON:0000073!4.87e-13!94;UBERON:0001016!4.87e-13!94;UBERON:0000468!7.71e-13!659;UBERON:0000922!3.59e-12!612;UBERON:0004119!6.55e-12!169;UBERON:0000925!6.55e-12!169;UBERON:0006595!6.55e-12!169;UBERON:0003080!1.57e-11!42;UBERON:0000119!2.72e-11!312;UBERON:0002780!4.28e-11!41;UBERON:0001890!4.28e-11!41;UBERON:0006240!4.28e-11!41;UBERON:0004111!5.64e-11!241;UBERON:0000483!6.93e-11!309;UBERON:0002050!6.95e-11!605;UBERON:0005423!6.95e-11!605;UBERON:0000923!1.66e-10!604;UBERON:0005291!1.66e-10!604;UBERON:0006598!1.66e-10!604;UBERON:0002532!1.66e-10!604;UBERON:0003056!4.71e-10!61;UBERON:0002020!6.88e-10!34;UBERON:0003528!6.88e-10!34;UBERON:0001893!8.31e-10!34;UBERON:0000477!1.35e-09!286;UBERON:0002791!1.71e-09!33;UBERON:0001869!3.84e-09!32;UBERON:0001007!1.29e-08!155;UBERON:0001555!1.29e-08!155;UBERON:0007026!1.29e-08!155;UBERON:0005631!1.21e-07!14;UBERON:0000158!1.21e-07!14;UBERON:0005156!2.05e-07!59;UBERON:0000990!2.05e-07!59;UBERON:0000956!2.18e-07!25;UBERON:0000203!2.18e-07!25;UBERON:0002619!3.37e-07!22;UBERON:0000464!3.43e-07!104;UBERON:0003076!4.36e-07!15;UBERON:0003057!4.36e-07!15;UBERON:0005177!4.49e-07!107;UBERON:0001008!4.55e-07!45;UBERON:0000466!6.67e-07!126
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}}
}}

Revision as of 14:39, 19 October 2012


Full id: C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:116164244..116164268,-p1@AFAP1L2
Hg19::chr10:116164270..116164290,-p2@AFAP1L2
Hg19::chr10:116164538..116164562,-p3@AFAP1L2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.60e-1242
epithelial cell1.88e-11253
endodermal cell4.98e-0958
respiratory epithelial cell3.19e-0713
Uber Anatomy
Ontology termp-valuen
adult organism3.54e-23114
organ part4.01e-16218
ecto-epithelium5.77e-15104
ectoderm-derived structure1.25e-14171
ectoderm1.25e-14171
presumptive ectoderm1.25e-14171
organ1.71e-14503
organ system subdivision2.26e-14223
central nervous system3.92e-1481
neural tube7.47e-1456
neural rod7.47e-1456
future spinal cord7.47e-1456
neural keel7.47e-1456
brain3.79e-1368
future brain3.79e-1368
regional part of nervous system1.09e-1253
regional part of brain1.09e-1253
anatomical cluster1.36e-12373
neural plate4.46e-1282
presumptive neural plate4.46e-1282
multi-tissue structure1.06e-11342
nervous system2.34e-1189
embryo3.29e-11592
neurectoderm1.39e-1086
anatomical system1.58e-10624
anatomical group2.23e-10625
multi-cellular organism2.32e-10656
structure with developmental contribution from neural crest5.48e-10132
endoderm-derived structure6.30e-10160
endoderm6.30e-10160
presumptive endoderm6.30e-10160
developing anatomical structure7.51e-10581
renal system9.94e-0948
regional part of forebrain1.63e-0841
forebrain1.63e-0841
anterior neural tube1.63e-0841
future forebrain1.63e-0841
anatomical conduit1.81e-08240
cell layer2.08e-08309
epithelium2.63e-08306
urinary system structure3.17e-0847
extraembryonic membrane7.03e-0814
membranous layer7.03e-0814
brain grey matter8.23e-0834
gray matter8.23e-0834
telencephalon9.79e-0834
embryonic structure1.91e-07564
regional part of telencephalon2.95e-0732
pre-chordal neural plate3.14e-0761
cerebral hemisphere3.42e-0732
posterior neural tube3.77e-0715
chordal neural plate3.77e-0715
reproductive organ4.18e-0748
reproductive structure6.01e-0759
reproductive system6.01e-0759
trunk region element9.16e-07101
digestive system9.21e-07145
digestive tract9.21e-07145
primitive gut9.21e-07145
Disease
Ontology termp-valuen
squamous cell carcinoma1.56e-0714


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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